OK, I just figured out how to trap that server up-service-down problem using
PING. (for http file reading, PHP apparently doesn't properly set its
timeout until AFTER a connection has been made and the file is
streaming.)I'm a little wary of switching modes behind the scenes. For
Wikipedia, I'm not interested in retrieving a 2D instead of a 3D. I don't
see the point of that. I presume ChemSpider is a lookup as well.
What we really need is a mirror for the NIH site.
Bob
On Mon, Apr 25, 2011 at 10:29 AM, Otis Rothenberger
<[email protected]>wrote:
> Bob,
>
> I should mention that I now have a viable route from SMILES ----> PubChem
> SDF that is independent of Resolver translations. The SDF is a look up and
> not as desirable as Resolver, but it might be a good back-up option. Here's
> the route:
>
> SMILES to Standard InChI via ChemSpider
> Standard InChI to PubChem CID via PubChem
> CID to SDF via PubChem
>
> I have this set up on the JME Draw Screen of our application at:
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> Issues:
> 1) I should grab 2D SDF if the 3D is not available. This is easy to do. I
> just don't have it set up yet.
> 2) PubChem occasionally has some priority nuttiness (e.g. hydron phenoxide
> comes up with a higher priority than phenol on an InChI query). This type of
> nuttiness is trappable.
>
> The issues are, well issues, but we're talking back-up here.
>
> The ChemSpider trip is:
>
> http://www.chemspider.com/InChI.asmx/SMILESToInChI?smiles=CCCC(O)C
>
> Very fast - xml return:
> <string>InChI=1S/C5H12O/c1-3-4-5(2)6/h5-6H,3-4H2,1-2H3</string>
>
> After parsing, you have to keep the InChI= and wrap the whole thing is
> %22's for PubChem.
>
>
> Otis
>
> --
> Otis Rothenberger
> Department of Chemistry
> Illinois State University Normal, IL 61790-4160
> http://chemagic.org
>
> ------------------------------
> *From*: "Robert Hanson" <[email protected]>
> *Sent*: Monday, April 25, 2011 10:58 AM
> *To*: [email protected], [email protected]
> *Subject*: Re: [Jmol-users] Wikipedia
>
>
> Right -- product of conversations with Martin Walker at the ACS meeting.
> See also
>
> http://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Chemicals#Comments
>
> (but the service is unavailable at this time)
>
> On Sun, Apr 24, 2011 at 10:40 PM, Otis Rothenberger <[email protected]
> > wrote:
>
>> All-
>>
>> I kind of lost track of this. It looks like Wikipedia has implemented Jmol
>> off of SMILES - e.g.
>>
>> http://en.wikipedia.org/wiki/Chalcone
>>
>> A one month conversion!
>>
>> Otis
>>
>> --
>> Otis Rothenberger
>> Department of Chemistry
>> Illinois State University Normal, IL 61790-4160
>> http://chemagic.org
>>
>> ------------------------------------------------------------------------------
>> Fulfilling the Lean Software Promise
>> Lean software platforms are now widely adopted and the benefits have been
>> demonstrated beyond question. Learn why your peers are replacing JEE
>> containers with lightweight application servers - and what you can gain
>> from the move. http://p.sf.net/sfu/vmware-sfemails
>> _______________________________________________
>> Jmol-users mailing list
>> [email protected]
>> https://lists.sourceforge.net/lists/listinfo/jmol-users
>>
>>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
>
>
> ------------------------------------------------------------------------------
> Fulfilling the Lean Software Promise
> Lean software platforms are now widely adopted and the benefits have been
> demonstrated beyond question. Learn why your peers are replacing JEE
> containers with lightweight application servers - and what you can gain
> from the move. http://p.sf.net/sfu/vmware-sfemails
> _______________________________________________
> Jmol-users mailing list
> [email protected]
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
------------------------------------------------------------------------------
Fulfilling the Lean Software Promise
Lean software platforms are now widely adopted and the benefits have been
demonstrated beyond question. Learn why your peers are replacing JEE
containers with lightweight application servers - and what you can gain
from the move. http://p.sf.net/sfu/vmware-sfemails
_______________________________________________
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